Mercurial > repos > iracooke > tpp_prophets

changeset 2:5674c9c2e0d0

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Update
author Ira Cooke <iracooke@gmail.com>
date Sun, 09 Jun 2013 08:32:54 -0500
parents a9f016a531a5
children ffe1e8b1d6c3
files interprophet.xml peptide_prophet.xml pepxml_to_table.xml protein_prophet.xml
diffstat 4 files changed, 60 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/interprophet.xml	Thu Jun 06 15:37:51 2013 +1000
+++ b/interprophet.xml	Sun Jun 09 08:32:54 2013 -0500
@@ -8,10 +8,23 @@
 
   <description>Combine Peptide Prophet results from multiple search engines</description>
 
-  <command interpreter="ruby">
+  <command interpreter="bash">
+
+	interprophet_wrapper.sh 
+
+	$output 
+
+	$use_nss 
 
-	interprophet_wrapper.rb $output $use_nss $use_nrs $use_nse $use_nsi $use_nsm --minprob $minprob
+	$use_nrs 
+
+	$use_nse 
 
+	$use_nsi 
+
+	$use_nsm 
+
+	--minprob $minprob
 
 	## Inputs.
 	${first_input}
@@ -29,11 +42,11 @@
 		<param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/>
 	</repeat>
 	
-	<param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--nonss"/>
-	<param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--nonrs"/>
-	<param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--nonse"/>
-	<param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--nonsi"/>
-	<param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--nonsm"/>
+	<param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--no-nss"/>
+	<param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--no-nrs"/>
+	<param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--no-nse"/>
+	<param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--no-nsi"/>
+	<param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--no-nsm"/>
 	
 	<param name="minprob" type="text" label="Minimum threshod probability for reporting results"/>
 		
--- a/peptide_prophet.xml	Thu Jun 06 15:37:51 2013 +1000
+++ b/peptide_prophet.xml	Sun Jun 09 08:32:54 2013 -0500
@@ -6,7 +6,24 @@
    
 	<description>Calculate Peptide Prophet statistics on search results</description>
 
-	<command interpreter="ruby">peptide_prophet_wrapper.rb ${output} ${input_file}  -r $glyco $useicat $phospho $usepi $usert $accurate_mass $no_ntt $no_nmc $use_gamma $use_only_expect $force_fit $allow_alt_instruments $maldi
+	<command interpreter="bash">
+        peptide_prophet_wrapper.sh $output $input_file
+
+        -r 
+        $glyco 
+        $useicat 
+        $phospho 
+        $usepi 
+        $usert 
+        $accurate_mass 
+        $no_ntt 
+        $no_nmc 
+        $use_gamma 
+        $use_only_expect 
+        $force_fit 
+        $allow_alt_instruments 
+        $maldi
+
 	</command>
 
 	<inputs>
--- a/pepxml_to_table.xml	Thu Jun 06 15:37:51 2013 +1000
+++ b/pepxml_to_table.xml	Sun Jun 09 08:32:54 2013 -0500
@@ -15,7 +15,7 @@
 
 <inputs>
 
-	<param name="input_file" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>
+	<param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>
 
 </inputs>
 <outputs>
--- a/protein_prophet.xml	Thu Jun 06 15:37:51 2013 +1000
+++ b/protein_prophet.xml	Sun Jun 09 08:32:54 2013 -0500
@@ -8,7 +8,27 @@
 
 
 <!-- Note .. the input file is assumed to be the first argument -->
-  <command interpreter="ruby">protein_prophet_wrapper.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command>
+  <command interpreter="bash">
+  	protein_prophet_wrapper.sh 
+
+  	--galaxy $input_file 
+
+  	-r
+
+  	$iproph 
+  	$nooccam 
+  	$groupwts 
+  	$normprotlen 
+  	$logprobs 
+  	$confem 
+  	$allpeps 
+  	$unmapped 
+  	$instances 
+  	$delude
+  	
+  	--minprob=$minprob 
+  	--minindep=$minindep 
+  </command>
   <inputs>
 	
     <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/>